I've had fittings on both my bikes. I ordered what my fitter called a neutral fit on my road bike and a touring fit on my LHT. I'm not sure if those are official terms but the way he explained it to me the touring fit in particular means more upright and using the quads.
I feel like I only use my quads on both bikes really. I want to train for a pretty long distance ride this year and I'd like to improve my climbing. I'm wondering if in the long run it might be beneficial to work other muscles (hams, calves, etc..) while training and how to adjust my bike fit to do so?
I have a few more questions:
I realize the pedal axle should be under the ball of my foot but how do I determine the left/right position (in other words the cleats can move not only forward and back but also slide to the side).
should I always keep my knees straight or angle them (for instance knee in towards the TT)? I have a lightly torn ACL and want to get the best knee position.
When I watch other riders pedal I notice some of them 'scoop' their foot as they start the upstroke while others don't. Is one method better than the other or is it just a personal choice?
On training... I don't have a lot of time these days but need to train for a distance ride in June. I need to improve my climbing and speed (I'm still pretty much a beginner speed-wise). I want to do hill repeats and big ring riding on weekdays for a short time every morning and one distance cardio ride on weekends. Should I do hills/mashing every other day and just ride light on odd days or do hills/mashing every weekday. How much should I ramp up my distance rides each week (10% sound reasonable?)

If your position has your knee over the pedal spindle, you can move the seat back a bit so your knee is 1-2cm behind the pedal spindle. That engages the glutes more, especially when climbing. It's not going to take a slow climber and make him fast however.

I set foot angle by paying attention to my feet while I ride. If it feels like I want to rotate the foot to a different position I adjust the cleat to allow it. Everyone is different but most likely your best position will have your knees more or less in line with the pedals, neither bow legged or hitting the top tube all the time. Heels in makes you more bow legged, heels out moves the knees in.

I don't beleive that a recreational rider needs to do big gear repeats. (I'm a racer and don't do them). Unless you have a good base and strong knees from years of riding you are more likely to injure yourself, and the training benefit over just riding hills is not all that appropriate for recreational riding. If it even exists at all- there is a big argument among exercise physiologists if big gear repeats have any benefit at all vs self-selected cadence. Your limit right now is your endurance base, so just go ride more. Include hills of course if you want to work on your climbing.

Wow, that's a lot of questions, all good ones.
I believe very strongly that it is beneficial to pedal with more leg muscles. The more one spreads out the work, the longer the muscles last. If one's bike fit is good, it will allow most any riding modality. Bike fit is a compromise. As your fitter pointed out, the trick is to have the compromise tilted toward the riding which you will do on that bike. What you are talking about is learning to "pedal circles." It's actually easier to pedal circles in a more upright position than on the drops, for instance. I think your fitter has it backwards about that. The main reason given for the common more upright touring fit is that one doesn't need to be as aero, as speeds are lower, so why not sit in a position that allows better breathing and leg mechanics? Yeah, tell that to the tourer who's battled headwinds for a week. Personally, I like the same position for everything except TT.

Most people find a lower Q factor (feet closer together) to be easier on the legs. Depending on how one's feet sit on the pedals, and one's bike geometry, one may have to watch for heel strike on the chainstays or crank. Personally, I pronate slightly when I walk, but have trained myself to bike with feet straight fore-and-aft. I find that kinder to my knees.

It's faster to pedal knees in. Aero testing tells us that pedaling knees in gives the same drag reduction as a set of high zoot racing wheels. However, not everyone's knees take kindly to that. It's generally recommended to keep the knee centered over the foot. That said, I know a number of long distance cyclists who pedal knees in all the time, even climbing. I also know some who pedal with knees way out. So it's all in what you got in the way of knees. One thing to watch is to try not to have side-to-side movement of the knees during the pedal stroke. That seems to be associated with some overuse syndromes.

In thinking about a good pedal stroke, think about applying a constant torque to the bottom bracket. This means always having power coming from one foot or the other, or both at a reduced force, all the way around the stroke. I find it best to concentrate on pulling the foot back at the bottom and then back and up for maybe another 30°, until the ham becomes ineffective. Your other foot will carry the load while that one comes over the top, so just take the weight out of the pedal, maybe push forward a little as it comes over the top. One doesn't need to concentrate on pushing down, as that seems to happen by itself.

There are four drills that make all the difference in climbing for me:
1) FastPedal. One warms up for 15' in zone 1, then pedals at a very high cadence, 115-120 if possible, however at a heart rate no higher than the top of zone 2, meaning that one can still speak in complete sentences but will breathe deeply and sweat. One does this continuously for 15-45 minutes, no break. One uses very low gears for this, setting the gearing with high cadence as first priority. If one can attain the cadence but effort is too low, one can increase the gearing. If one is out of shape, this may limit one to a max cadence of 100. Just keep at it, once/week. This almost has to be done on the trainer or rollers as it's hard to find the right road for it.
2) One-legged pedaling. Again on trainer or rollers. Pedal for 2 minutes with one foot, then the other, then legs together. Repeat for 15 to 45 minutes, continuously. Same warmup as for FastPedal. I like to pedal 50-55 and 80-85 cadence in alternate sets. The chain must remain taut the whole pedal stroke. If it goes slack on the backstroke, stop with that leg and switch to the other.
3) Low cadence climbing. Find a 10 minute hill and climb it at 50-55 cadence in the tempo zone (zone 3). Effort hard, but not extreme. No upper body movement at all, no prying on the bars. 3-4 repeats.
4) High cadence riding in easy rollers. Find a section of slightly rolling road about 30 minutes long. Ride it in the tempo zone at least at 100 cadence. Hold the cadence and effort as even as you can, uphill and down, the whole way. You'll have to shift a lot. Take 5 minutes of easy pedaling and head back, same thing again.

Notice that all of these drills are about becoming more efficient. I find that most people can get plenty of hard hills in their normal riding, so focusing on drills like these listed is a huge help. In my early season training, I do a few weeks of each of these drills, one once a week for maybe a month, in the order listed. Actually, since I start my training year in November, I get more than a month of the first two. Other than these drills, do normal, moderate rides, say 20 miles each, during the week as your recovery allows.

If you want to train for a distance ride, now is well into the time to start riding distance, once a week. 10% is plenty and compounds faster than you'd like it to. Just ride it moderate, zone 2, maybe a little zone 3 on the hills, but hold it down. That doesn't mean ride easy. Zone 2 is not easy, just well below the effort that produces leg pain. By now, you should be riding 60 miles or so on your long ride. Very gradually, increase your pace on the hills. About the last 6 weeks before your event, start doing the harder intervals or pass repeats, depending on the nature of your target ride. Depending on the length of your target ride, you should eventually be riding at least that ride length in total mileage per week, with a maximum necessary weekly mileage of 180-240, depending on your recovery ability.

Wow that was helpful. It's like having a personal trainer. Thanks so much. ericm979, To kind of explain myself about why I want to experiment with engaging other muscles; I think you're right, I don't think using other muscles will make me a faster climber. But I am kind of hoping that if I don't put 100% of my work into just one muscle I might be able to share some of the work load and possible last longer.

I had guessed that moving the saddle back slightly might increase reliance on the gluts. It's a shame my brooks seems to be about as far back as it can go. Those b17s have a short rail. Thanks for the warning on big gears. Since my knee has attitude I should probably be careful.

Carbonfiberboy thanks for all the tips. It makes sense that I should work on pedal form and efficiency in general. If for nothing else it may lessen the chance of my ACL acting up. I'm certainly going to work on it and thanks for the detailed drills.

Eric is right about the low cadence drills: if they hurt your knees, don't do them. They assume at least a couple of years of prior training. However the smoothness that is the focus of these drills may actually help your knees by improving your form. By the time you get to them in April, your conditioning might be up to them. Then the high cadence road drills in May. I used to have bad knees, but cycling has fixed them. Not a torn ACL, though.